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{{f5samples
{{f5samples
|id=FF:10059-101H5
|ancestors_in_anatomy_facet=UBERON:0000005,UBERON:0000020,UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000073,UBERON:0000153,UBERON:0000165,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000925,UBERON:0000930,UBERON:0001007,UBERON:0001016,UBERON:0001032,UBERON:0001033,UBERON:0001062,UBERON:0001444,UBERON:0001555,UBERON:0001723,UBERON:0002050,UBERON:0002532,UBERON:0002539,UBERON:0003212,UBERON:0004119,UBERON:0004121,UBERON:0004362,UBERON:0004456,UBERON:0005423,UBERON:0005726,UBERON:0006260,UBERON:0006756,UBERON:0006757,UBERON:0007026,UBERON:0008814,UBERON:0008816
|name=tongue, fetal, donor1
|sample_id=10059
|rna_tube_id=101H5
|rna_box=101
|rna_position=H5
|sample_cell_lot=NA
|sample_cell_catalog=NA
|sample_company=Biochain
|rna_lot_number=B301061
|rna_catalog_number=Cat:RtHFN: Tongue
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=32 weeks fetus
|sample_tissue=tongue
|sample_donor(cell lot)=1
|sample_sex=female
|sample_age=
|sample_ethnicity=A?
|rna_rin=9.3
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_cell_line=
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=normal
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_weight_ug=50
|rna_concentration=2
|sample_note=
|profile_hcage=CNhs11768,LSID820,release009,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000005,UBERON:0000020,UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000073,UBERON:0000153,UBERON:0000165,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000925,UBERON:0000930,UBERON:0001007,UBERON:0001016,UBERON:0001032,UBERON:0001033,UBERON:0001062,UBERON:0001444,UBERON:0001555,UBERON:0001723,UBERON:0002050,UBERON:0002532,UBERON:0002539,UBERON:0003212,UBERON:0004119,UBERON:0004121,UBERON:0004362,UBERON:0004456,UBERON:0005423,UBERON:0005726,UBERON:0006260,UBERON:0006756,UBERON:0006757,UBERON:0007026,UBERON:0008814,UBERON:0008816
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 33:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
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|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:10059-101H5
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010059
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010059
|name=tongue, fetal, donor1
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11768,LSID820,release009,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=101
|rna_catalog_number=Cat:RtHFN: Tongue
|rna_concentration=2
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_lot_number=B301061
|rna_od260/230=
|rna_od260/280=
|rna_position=H5
|rna_rin=9.3
|rna_sample_type=total RNA
|rna_tube_id=101H5
|rna_weight_ug=50
|sample_age=
|sample_cell_catalog=NA
|sample_cell_line=
|sample_cell_lot=NA
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=Biochain
|sample_description=
|sample_dev_stage=32 weeks fetus
|sample_disease=normal
|sample_donor(cell lot)=1
|sample_ethnicity=A?
|sample_experimental_condition=
|sample_id=10059
|sample_note=
|sample_sex=female
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=tongue
|top_motifs=MEF2{A,B,C,D}:6.47186095528;TBP:4.19155801896;NR6A1:3.7256144065;ZNF384:3.53802479752;HOX{A4,D4}:3.46784429997;FOXL1:3.36227896513;TFAP4:3.33777733567;TAL1_TCF{3,4,12}:3.32870855602;NR1H4:3.21835617946;NR5A1,2:3.18768977158;SOX5:3.15271344177;MYOD1:2.87490965537;IKZF2:2.73581952997;ESR1:2.71440259389;KLF4:2.65009404056;GATA4:2.32602788;NFE2L1:2.27439608659;MYBL2:2.2274092384;SPZ1:2.22656777173;ZIC1..3:2.08387787022;IKZF1:2.08303882847;SRF:2.01214719722;LMO2:1.92520257639;FOXQ1:1.91965534159;TBX4,5:1.85944013488;FOXM1:1.85779094819;GCM1,2:1.83188315853;TFAP2{A,C}:1.82064880258;ESRRA:1.74362521677;NKX2-3_NKX2-5:1.6537765586;RXR{A,B,G}:1.62147500071;NKX2-1,4:1.61657720806;ZNF423:1.60096288755;TGIF1:1.57209422169;SNAI1..3:1.56273605775;NHLH1,2:1.55772798062;GLI1..3:1.55248845753;TFCP2:1.54466917966;MAZ:1.53165227528;SMAD1..7,9:1.51691157444;POU3F1..4:1.50104549977;UFEwm:1.49125126707;HAND1,2:1.46648748781;ALX4:1.37299962984;NKX2-2,8:1.36988115086;MAFB:1.36008203309;ATF2:1.34919350361;GTF2A1,2:1.34501117916;PATZ1:1.25372640655;CDC5L:1.24287576967;RXRA_VDR{dimer}:1.2082460266;CUX2:1.19722463292;HIC1:1.16426739562;RBPJ:1.15681877842;NFIX:1.12641312586;HSF1,2:1.11874864132;TLX1..3_NFIC{dimer}:1.11153025822;PAX6:1.109655828;LHX3,4:1.0856838948;TLX2:1.06488640248;XBP1:1.0626898957;ZNF148:1.04415853114;TEF:1.03832811186;RREB1:1.02920828836;NKX6-1,2:0.986916793725;MED-1{core}:0.985543536521;PAX5:0.968770267715;ZBTB6:0.936892907848;PDX1:0.933917237533;SP1:0.919139634213;CDX1,2,4:0.91844681264;POU1F1:0.917134869592;ZNF238:0.897068785091;MTF1:0.881876388114;NFATC1..3:0.855095180209;TEAD1:0.853921305113;ALX1:0.85290351981;YY1:0.844984524374;ZEB1:0.830192297669;HMX1:0.801388030093;FOXO1,3,4:0.771953790562;FOXP3:0.759522063143;TP53:0.733210275326;NR3C1:0.719572051642;NANOG{mouse}:0.707649782322;GTF2I:0.706514324095;PAX1,9:0.676301116408;ARID5B:0.667935603213;BPTF:0.655360954833;EVI1:0.649153679774;MYFfamily:0.647402198309;NKX3-2:0.634463240952;TOPORS:0.577949246766;PBX1:0.577450481875;PPARG:0.568210786199;AR:0.548295029832;POU6F1:0.547462987886;IRF7:0.54098684326;EGR1..3:0.523095784638;HOX{A6,A7,B6,B7}:0.482040149184;MZF1:0.472160195394;PRDM1:0.460203601167;HES1:0.451414750466;NKX3-1:0.444192205044;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.422351747646;TFAP2B:0.40473232339;SOX{8,9,10}:0.388535779275;FOX{F1,F2,J1}:0.384806759935;ONECUT1,2:0.336749124198;REST:0.306963771266;JUN:0.287037972541;ATF6:0.264474513346;FOXA2:0.255297684464;ZBTB16:0.162140017957;RORA:0.132634098863;LEF1_TCF7_TCF7L1,2:0.110692216319;MTE{core}:0.0890326145294;RFX2..5_RFXANK_RFXAP:0.0555950362321;EP300:0.0471731871375;XCPE1{core}:-0.0616286336691;ZNF143:-0.0649207226608;FOXN1:-0.0811938458964;GFI1:-0.0832013350558;ZFP161:-0.0838829067234;ATF4:-0.0923403371139;AIRE:-0.0925992185142;GFI1B:-0.117466668154;SOX2:-0.130045826951;SOX17:-0.132255259893;FOSL2:-0.136151405768;STAT5{A,B}:-0.141622078332;BREu{core}:-0.150182249874;POU5F1:-0.152918225986;FOXP1:-0.224208528031;HNF4A_NR2F1,2:-0.272128133022;DMAP1_NCOR{1,2}_SMARC:-0.318896868753;ETS1,2:-0.333353123189;SPI1:-0.335347678374;HOX{A5,B5}:-0.343429023642;NANOG:-0.344460483715;PAX3,7:-0.355081617056;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.432734119864;NRF1:-0.436301730595;IRF1,2:-0.443002432141;PAX4:-0.445121931896;NFY{A,B,C}:-0.445411189782;FOX{I1,J2}:-0.457807444973;CREB1:-0.470501913039;PITX1..3:-0.479418207166;HMGA1,2:-0.493136768293;FOS_FOS{B,L1}_JUN{B,D}:-0.502113209322;PAX2:-0.502423930689;HLF:-0.504987823998;SPIB:-0.506691244163;CRX:-0.52305268016;E2F1..5:-0.527054773846;GZF1:-0.529338873007;STAT1,3:-0.571804078098;T:-0.592805747778;ELF1,2,4:-0.595023986972;NFKB1_REL_RELA:-0.624584894024;CEBPA,B_DDIT3:-0.657600746854;FOX{D1,D2}:-0.661961107578;SREBF1,2:-0.670317129321;GATA6:-0.686171797903;NFIL3:-0.708855012116;BACH2:-0.720207586311;ATF5_CREB3:-0.743920934007;HNF1A:-0.765248101901;STAT2,4,6:-0.780080032243;EBF1:-0.789782051267;NFE2:-0.803138266396;HOXA9_MEIS1:-1.0336960291;RFX1:-1.04214380921;FOXD3:-1.05103012813;OCT4_SOX2{dimer}:-1.06612409391;RUNX1..3:-1.15371008136;DBP:-1.15934233475;TFDP1:-1.15941901255;ADNP_IRX_SIX_ZHX:-1.17613678894;EN1,2:-1.20799057549;HIF1A:-1.23287913867;NFE2L2:-1.23458359047;bHLH_family:-1.26579862336;POU2F1..3:-1.37850001347;VSX1,2:-1.41821340189;HBP1_HMGB_SSRP1_UBTF:-1.41909289611;ELK1,4_GABP{A,B1}:-1.5240827322;AHR_ARNT_ARNT2:-1.56809661644;PRRX1,2:-1.61811855934;MYB:-1.72248091771;PAX8:-1.73879167121
}}
}}

Revision as of 14:01, 21 March 2012


Name:tongue, fetal, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuetongue
dev stage32 weeks fetus
sexfemale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberB301061
catalog numberCat:RtHFN: Tongue
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]





Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0.404
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.121
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs11768

Jaspar motifP-value
MA0002.20.00532
MA0003.10.147
MA0004.10.0018
MA0006.10.147
MA0007.10.157
MA0009.10.121
MA0014.10.804
MA0017.10.741
MA0018.20.047
MA0019.10.0998
MA0024.10.0808
MA0025.10.321
MA0027.10.879
MA0028.12.48438e-7
MA0029.10.583
MA0030.10.482
MA0031.10.0857
MA0035.20.0856
MA0038.10.122
MA0039.20.333
MA0040.11
MA0041.10.721
MA0042.10.671
MA0043.10.00136
MA0046.10.00416
MA0047.20.48
MA0048.15.86756e-4
MA0050.17.54576e-5
MA0051.14.56068e-4
MA0052.16.14219e-28
MA0055.10.00207
MA0057.10.469
MA0058.16.62782e-5
MA0059.10.00233
MA0060.10.00162
MA0061.11.57204e-5
MA0062.25.22692e-16
MA0065.20.622
MA0066.10.296
MA0067.10.0637
MA0068.10.0975
MA0069.10.829
MA0070.10.662
MA0071.10.986
MA0072.10.552
MA0073.10.279
MA0074.10.736
MA0076.13.86243e-9
MA0077.10.705
MA0078.10.336
MA0079.20.698
MA0080.22.00174e-8
MA0081.18.11094e-4
MA0083.10.0309
MA0084.10.241
MA0087.10.0568
MA0088.10.0609
MA0090.10.43
MA0091.10.0119
MA0092.10.472
MA0093.10.00129
MA0099.26.36756e-13
MA0100.10.0107
MA0101.16.83668e-5
MA0102.28.26436e-4
MA0103.10.0502
MA0104.23.45625e-5
MA0105.10.00154
MA0106.10.101
MA0107.11.47851e-4
MA0108.29.55581e-19
MA0111.10.436
MA0112.20.00205
MA0113.10.0536
MA0114.10.774
MA0115.10.692
MA0116.10.119
MA0117.10.395
MA0119.10.3
MA0122.10.225
MA0124.10.396
MA0125.10.688
MA0131.10.12
MA0135.10.816
MA0136.18.89097e-12
MA0137.20.056
MA0138.20.194
MA0139.10.0475
MA0140.10.0359
MA0141.10.427
MA0142.10.0143
MA0143.10.319
MA0144.10.196
MA0145.10.0358
MA0146.10.962
MA0147.15.95476e-5
MA0148.10.564
MA0149.10.0987
MA0150.13.08729e-7
MA0152.10.329
MA0153.10.813
MA0154.10.838
MA0155.10.0856
MA0156.11.91348e-15
MA0157.10.0335
MA0159.10.196
MA0160.10.88
MA0162.10.0906
MA0163.10.13
MA0164.10.726
MA0258.10.0236
MA0259.10.0587



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs11768

Novel motifP-value
10.804
100.158
1000.358
1010.781
1020.703
1030.661
1040.749
1050.523
1060.354
1070.0193
1080.129
1090.302
110.951
1100.904
1110.649
1120.273
1137.79414e-4
1140.652
1150.0231
1160.146
1170.0896
1180.0782
1190.278
120.763
1200.55
1210.99
1220.0216
1230.0582
1240.0276
1250.624
1260.684
1270.824
1280.371
1290.718
130.913
1300.544
1310.51
1320.0408
1330.147
1340.146
1350.263
1360.663
1370.356
1380.542
1390.513
140.894
1400.387
1410.892
1420.786
1430.0351
1440.875
1450.684
1460.802
1470.00712
1480.366
1490.0304
150.236
1500.833
1510.562
1520.128
1530.327
1540.77
1550.383
1560.561
1570.495
1580.364
1590.616
160.213
1600.439
1610.488
1620.238
1630.159
1640.235
1650.0637
1660.131
1670.143
1680.859
1690.0455
170.98
180.306
190.00933
20.0861
200.0101
210.467
220.231
230.324
240.0648
250.892
260.624
270.855
280.622
290.14
30.637
300.00311
310.403
326.18702e-4
330.787
340.723
350.714
360.0581
370.95
380.861
390.269
40.774
400.406
410.352
420.3
430.479
440.00379
450.0942
460.883
470.52
480.627
490.529
50.573
500.804
510.89
520.193
530.802
540.668
550.326
560.579
570.717
580.938
590.372
60.924
600.223
610.68
620.767
630.39
640.596
650.495
660.0283
670.152
680.178
690.277
70.608
700.938
710.25
720.605
730.569
740.145
750.444
760.0648
770.0466
780.224
790.162
80.915
800.336
810.168
820.539
830.926
840.366
850.00209
860.776
870.137
880.507
890.0317
90.861
900.0966
910.217
920.511
930.883
940.127
950.0953
960.914
970.621
980.955
990.0189



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs11768


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

UBERON: Anatomy
0000020 (sense organ)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000165 (mouth)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000925 (endoderm)
0000930 (stomodeum)
0001007 (digestive system)
0001016 (nervous system)
0001032 (sensory system)
0001033 (gustatory system)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001555 (digestive tract)
0001723 (tongue)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0002539 (pharyngeal arch)
0004119 (endoderm-derived structure)
0004121 (ectoderm-derived structure)
0004362 (pharyngeal arch 1)
0004456 (entire sense organ system)
0005423 (developing anatomical structure)
0007026 (primitive gut)
0008814 (pharyngeal arch system)
0008816 (embryonic head)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

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